Debbie Bard

Journal Articles

Antypas, KB and Bard, DJ and Blaschke, JP and Canon, RS and Enders, B and Shankar, M and Somnath, S and Stansberry, D and Uram, TD and Wilkinson, SR, "Enabling discovery data science through cross-facility workflows", Institute of Electrical and Electronics Engineers (IEEE), December 2021, 3671-3680, doi: 10.1109/bigdata52589.2021.9671421

Mustafa Mustafa, Deborah Bard, Wahid Bhimji, Rami Al-Rfou, Zarija Lukić, "Creating Virtual Universes Using Generative Adversarial Networks", Submitted To Sci. Rep., June 1, 2017,

Debbie Bard, Wahid Bhimji, David Paul, Glenn K Lockwood, Nicholas J Wright, Katie Antypas, Prabhat Prabhat, Steve Farrell, Andrey Ovsyannikov, Melissa Romanus, others, "Experiences with the Burst Buffer at NERSC", Supercomputing Conference, November 16, 2016, LBNL LBNL-1007120,

Download File: works-1.bib (bib: 9 KB)

Wahid Bhimji, Debbie Bard, Melissa Romanus, David Paul, Andrey Ovsyannikov, Brian Friesen, Matt Bryson, Joaquin Correa, Glenn K Lockwood, Vakho Tsulaia, others, "Accelerating science with the NERSC burst buffer early user program", Cray User Group, May 11, 2016, LBNL LBNL-1005736,

Download File: works-1.bib (bib: 9 KB)

NVRAM-based Burst Buffers are an important part of the emerging HPC storage landscape. The National Energy Research Scientific Computing Center (NERSC) at Lawrence Berkeley National Laboratory recently installed one of the first Burst Buffer systems as part of its new Cori supercomputer, collaborating with Cray on the development of the DataWarp software. NERSC has a diverse user base comprised of over 6500 users in 700 different projects spanning a wide variety of scientific computing applications. The use-cases of the Burst Buffer at NERSC are therefore also considerable and diverse. We describe here performance measurements and lessons learned from the Burst Buffer Early User Program at NERSC, which selected a number of research projects to gain early access to the Burst Buffer and exercise its capability to enable new scientific advancements. To the best of our knowledge this is the first time a Burst Buffer has been stressed at scale by diverse, real user workloads and therefore these lessons will be of considerable benefit to shaping the developing use of Burst Buffers at HPC centers.

Conference Papers

Deborah J. Bard, Mark R. Day, Bjoern Enders, Rebecca J. Hartman–Baker, John Riney III, Cory Snavely, Gabor Torok, "Automation for Data-Driven Research with the NERSC Superfacility API", Lecture Notes in Computer Science, Springer International Publishing, 2021, 333, doi: 10.1007/978-3-030-90539-2_22

B Enders, D Bard, C Snavely, L Gerhardt, J Lee, B Totzke, K Antypas, S Byna, R Cheema, S Cholia, M Day, A Gaur, A Greiner, T Groves, M Kiran, Q Koziol, K Rowland, C Samuel, A Selvarajan, A Sim, D Skinner, R Thomas, G Torok, "Cross-facility science with the Superfacility Project at LBNL", IEEE/ACM WND Annual Workshop on Extreme-scale Experiment-in-the-Loop Computig (XLOOP), 2020, pp. 1-7, doi: 10.1109/XLOOP51963.2020.00006., November 12, 2020, 00:1-7, doi: 10.1109/XLOOP51963.2020.00006.

Wahid Bhimji, Debbie Bard, Kaylan Burleigh, Chris Daley, Steve Farrell, Markus Fasel, Brian Friesen, Lisa Gerhardt, Jialin Liu, Peter Nugent, Dave Paul, Jeff Porter, Vakho Tsulaia, "Extreme I/O on HPC for HEP using the Burst Buffer at NERSC", Journal of Physics: Conference Series, December 1, 2017, 898:082015,

B Friesen, MMA Patwary, B Austin, N Satish, Z Slepian, N Sundaram, D Bard, DJ Eisenstein, J Deslippe, P Dubey, Prabhat, "Galactos: Computing the Anisotropic 3-Point Correlation Function for 2 Billion Galaxies", November 2017, doi: 10.1145/3126908.3126927

The nature of dark energy and the complete theory of gravity are two central questions currently facing cosmology. A vital tool for addressing them is the 3-point correlation function (3PCF), which probes deviations from a spatially random distribution of galaxies. However, the 3PCF's formidable computational expense has prevented its application to astronomical surveys comprising millions to billions of galaxies. We present Galactos, a high-performance implementation of a novel, O(N2) algorithm that uses a load-balanced k-d tree and spherical harmonic expansions to compute the anisotropic 3PCF. Our implementation is optimized for the Intel Xeon Phi architecture, exploiting SIMD parallelism, instruction and thread concurrency, and significant L1 and L2 cache reuse, reaching 39% of peak performance on a single node. Galactos scales to the full Cori system, achieving 9.8 PF (peak) and 5.06 PF (sustained) across 9636 nodes, making the 3PCF easily computable for all galaxies in the observable universe.

Tina Declerck, Katie Antypas, Deborah Bard, Wahid Bhimji, Shane Canon, Shreyas Cholia, Helen (Yun) He, Douglas Jacobsen, Prabhat, Nicholas J. Wright, "Cori - A System to Support Data-Intensive Computing", Cray User Group Meeting 2016, London, England, May 2016,

Download File: Cori-CUG2016.pdf (pdf: 4.4 MB)

Presentation/Talks

Deborah Bard, Burst Buffers: Early Experiences and Outlook, Supercomputing 2016, November 14, 2016,

The long-awaited Burst Buffer technology is now being deployed on major supercomputing systems, including new machines at NERSC, LANL, ANL, and KAUST. In this BOF, we discuss early experience with Burst Buffers from both a systems and a user’s perspective, including challenges faced and perspectives for future development. Short presentations from early adopters will be followed by general discussion with the audience. We hope that this BOF will attract interest and participation from end-users and software/hardware developers.

See www.burstbuffer.org for presentations.

Debbie Bard, Using Containers and HPC to Solve the Mysteries of the Universe, DockerCon 2016, June 27, 2016,

Container technology is being used to answer some of the biggest questions in science today - what is the Universe made of? How has it evolved over time? Scientists use vast quantities of data to study these questions, and analyzing this data requires Big Data solutions on high performance computing resources. In this talk we discuss why containers are being deployed on the Cori supercomputer at NERSC (the National Energy Research Scientific Computing center) to answer fundamental scientific questions. We will give examples of the use of Docker in simulating complex physical processes and analyzing experimental data in fields as diverse as particle physics, cosmology, astronomy, genomics and material science. We will demonstrate how container technology is being used to facilitate access to scientific computing resources by scientists from around the globe. Finally, we will discuss how container technology has the potential to revolutionize scientific publishing, and could solve the problem of scientific reproducibility.

Tina Declerck, Katie Antypas, Deborah Bard, Wahid Bhimji, Shane Canon, Shreyas Cholia, Helen (Yun) He, Douglas Jacobsen, Prabhat, Nicholas J. Wright, Cori - A System to Support Data-Intensive Computing, Cray User Group Meeting 2016, London, England, May 12, 2016,

Debbie Bard, Accelerating Science with the NERSC Burst Buffer Early User Program, Salishan Conference on High-Speed Computing, April 28, 2016,

NVRAM-based Burst Buffers are an important part of the emerging HPC storage landscape. The National Energy Research Scientific Computing Center (NERSC) at Lawrence Berkeley National Laboratory recently installed one of the first Burst Buffer systems as part of its new Cori supercomputer, collaborating with Cray on the development of the DataWarp software. NERSC has a diverse user base comprised of over 6500 users in 750 different projects spanning a wide variety of scientific applications, including climate modeling, combustion, fusion, astrophysics, computational biology, and many more. The potential applications of the Burst Buffer at NERSC are therefore also considerable and diverse.

I will discuss the Burst Buffer Early User Program at NERSC, which selected a number of research projects to gain early access to the Burst Buffer and exercise its different capabilities to enable new scientific advancements. I will present details of the program, in-depth performance results and lessons-learnt from highlighted projects.

Reports

Gerber, Richard; Hack, James; Riley, Katherine; Antypas, Katie; Coffey, Richard; Dart, Eli; Straatsma, Tjerk; Wells, Jack; Bard, Deborah; Dosanjh, Sudip, et al., "Crosscut report: Exascale Requirements Reviews", January 22, 2018,

Salman Habib, Robert Roser (HEP Leads), Richard Gerber, Katie Antypas, Katherine Riley, Tim Williams, Jack Wells, Tjerk Straatsma (ASCR Leads), A. Almgren, J. Amundson, S. Bailey, D. Bard, K. Bloom, B. Bockelman, A. Borgland, J. Borrill, R. Boughezal, R. Brower, B. Cowan, H. Finkel, N. Frontiere, S. Fuess, L. Ge, N. Gnedin, S. Gottlieb, O. Gutsche, T. Han, K. Heitmann, S. Hoeche, K. Ko, O. Kononenko, T. LeCompte, Z. Li, Z. Lukic, W. Mori, P. Nugent, C.-K. Ng, G. Oleynik, B. O'Shea, N. Padmanabhan, D. Petravick, F.J. Petriello, J. Power, J. Qiang, L. Reina, T.J. Rizzo, R. Ryne, M. Schram, P. Spentzouris, D. Toussaint, J.-L. Vay, B. Viren, F. Wurthwein, L. Xiao, "ASCR/HEP Exascale Requirements Review Report", arXiv:1603.09303 [physics.comp-ph], March 31, 2016,

Posters

Annette Greiner, Evan Racah, Shane Canon, Jialin Liu, Yunjie Liu, Debbie Bard, Lisa Gerhardt, Rollin Thomas, Shreyas Cholia, Jeff Porter, Wahid Bhimji, Quincey Koziol, Prabhat, "Data-Intensive Supercomputing for Science", Berkeley Institute for Data Science (BIDS) Data Science Faire, May 3, 2016,

Review of current DAS activities for a non-NERSC audience.